CHANGES IN VERSION 2.3.1
------------------------
BUG FIXES
* Function vecMin inside .filterJunctionBySample threw an error if every element in counts vector was larger than the filter. Now works correctly using pmin instead.
CHANGES IN VERSION 2.1.3
-------------------------
NEW CITATION
* ASpli was published on Bioinformatics
* https://doi.org/10.1093/bioinformatics/btab141
FEATURES
* binGenome now displays a progress bar when binning.
BUG FIXES
* gbCounts identifies correctly NA in junction's name
* minAnchor in jCounts was hardcoded so it had no impact on analysis. It is being passed correctly now.
CHANGES IN VERSION 2.1
-------------------------
NEW FUNCTIONS AND FUNCTIONALITIES
* New locus plot helper function .plotGenePattern.
* plots coverage, junctions and architecture
FEATURES
* Enhancement to the vignettes.
* Quick start section was modify in order to use gtf and bam files provided by ASpli package
* Add new section ASpli overview in vignette
BUG FIXES
* binGenome function assigns correctly bins located at the start and the end of each gene
* binGenome function calculates correctly gene range overlap
CHANGES IN VERSION 1.99.3
-------------------------
NEW FUNCTIONS AND FUNCTIONALITIES
* New parameters for gbCounts and jCounts functions:
* libType: to specify single end ("SE") or paired end ("PE") library
* strandMode:
- 0: strand of the pair is always *.
- 1: strand of the pair is strand of its first alignment
- 2: strand of the pair is strand of its last alignment.
CHANGES IN VERSION 1.99.1
-------------------------
NEW FUNCTIONS AND FUNCTIONALITIES
* For counting: gbCounts and jCounts. We add library type and strand-specificity parameters.
* For DU estimation: DUreport.norm and DUreport.offset
* For prepare DU reports: filterSignals, gbDUreport, integrateSignals, jDUreport, splicingReport and junctionsPJU
* For printing reports: exportIntegratedSignals, writeJDU and writeSplicingReport
FUNCTIONS DEPRECATED
* loadBAM: will be replaced by gbCounts. Bams files are proccesed one by one, according target object. It improves running time and memory usage
* readCounts: it is replaced by gbCounts
* AsDiscover: it is replaced by jCounts
* DUreport: it is replaced by gbDUreport and jDUreport
* mergeBinDUAS: has no direct replacement.
* plotGenomicRegions: has not direct replacement. There are new functions for exportiing results into HTML pages.
CHANGES IN VERSION 1.5.1
-------------------------
BUG FIXES
* readCounts supports identical gene names in different chromosomes.
* Fixed default value for minAnchor argument of readCounts code, man page
and vignette.
CHANGES IN VERSION 1.3.12
-------------------------
FEATURES
* Events named previously as 'as' are now names 'Undefined AS' for the sake
of clarity.
* Enhancement to the vignettes.
BUG FIXES
* Added verbose and filterWithContrasted arguments to DUreport method.
CHANGES IN VERSION 1.3.11
-------------------------
FEATURES
* Change the assigning of some 'ES*' events to 'as' events.
* Added verbose option of DUreportBinSplice method
* junctionDUReport methods changed to junctionDUreport to be consistent with
other methods names.
BUG FIXES
* Many corrections in the vignette and man pages.
* ZNF410_E013.gr.pdf file in vignettes/images was changed to
ZNF410_E013_gr.pdf to be correctly used in the latex code.
CHANGES IN VERSION 1.3.10
-------------------------
DOCUMENTATION
* Vignette is updated to reflect changes in objects, methods and functions.
Minor revisions are still required.
BUG FIXES
* PlotGenomicRegions now can make plots from unmerged bams correctly.
CHANGES IN VERSION 1.3.9
------------------------
BUG FIXES
* plotBins function now shows x-tick labels correctly.
CHANGES IN VERSION 1.3.8
------------------------
FEATURES
* PlotGenomicRegions do not requires an ASpliCounts object
CHANGES IN VERSION 1.3.8
------------------------
BUG FIXES
* AsDiscover and DUreport can handle conditions with one samples. Results
should be taken with care, but ASpli doesn't break.
CHANGES IN VERSION 1.3.7
------------------------
FEATURES
* Added functions to filter elements in ASpliCounts objects by read counts
and read density.
CHANGES IN VERSION 1.3.6
------------------------
FEATURES
* geneMode is the default mode of offset estimation.
CHANGES IN VERSION 1.2.1 / 1.3.1
------------------------
BUG FIXES
* AsDiscover() no longer contains mixed row data for some IR and IR* bins in
irPIR table.
* DUReport() calculates correctly junction ratio for junctions sharing their
end in junction.counts table.
* DUReport() no longer fails when there are no junctions that share their
start or end.
* reacCounts() requires an explicit targets argument, instead of taking it
from the global environment (in which may not exist with that name).
CHANGES IN VERSION 1.1.0
------------------------
NEW FEATURES
* New ASpli_binGenome.log file. It reports the number of features being processed
CHANGES IN VERSION 0.98
-------------------------
NEW FEATURES
* Multiple bins are reclassified using annotated junctions